← BioTransfer GEO Dataset Finder
GEO series

Skeletal dysplasia-causing mutations in TRPV4 alter the chondrocyte’s transcriptomic response to mechanical loading

GSE283659 Mus musculus (mouse) RNA-seq (gene expression) 71 samples Submitted 2024/12/10 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 71 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
71 samples: 18 conditions, mostly with about 4 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
Transient receptor potential vanilloid 4 (TRPV4) is a mechanosensitive ion channel highly expressed in chondrocytes that maintains cartilage homeostasis during development and throughout aging. Mutations in the channel cause a wide range of developmental disorders including skeletal dysplasias. The gain-of-function mutations V620I and T89I have been identified to lead to brachyolmia and metatropic dysplasia, respectively.
Read the full summary ↓
Although it is known these mutations suppress hypertrophic differentiation, the mechanisms by which they alter chondrocyte response to mechanical loading remain to be elucidated. To determine the effect of these mutations on chondrocyte mechanotransduction, tissue-engineered cartilage was derived from differentiated CRISPR-edited human induced pluripotent stem cells harboring the moderate V620I or severe T89I TRPV4 mutations. Tissue-engineered hiPSC-derived cartilage was then subjected compressive mechanical loading at physiological levels, and RNA-sequencing was used to assess the transcriptomic signatures of wildtype and mutant tissue-engineered cartilage. Our results demonstrate that the V620I and T89I mutations lead to reduced mechanoresponsiveness, characterized by a lower number of differentially expressed genes and diminished activation of genes downstream of TRPV4 signaling and contributing towards the process of endochondral ossification. Changes in extracellular matrix production and organization were found to contribute towards the phenotype in V620I chondrocytes, whereas dysregulated retinoic acid signaling was linked to T89I, and disrupted proliferation was common to both. Our findings suggest that dysfunctional mechanotransduction arising due to the V620I and T89I mutations contribute to the developmental phenotypes observed in their respective skeletal dysplasias, introducing potential pharmacologic targets for these conditions.
This dataset
Open GSE283659 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE283659_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1194993 and SRA study SRP549885. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
18 conditions, mostly with about 4 replicates each
Wildtype, free-swelling, sample ×4 Wildtype, loaded 24 hours, sample ×4 Wildtype, loaded 0 hours, sample ×4 Wildtype, free-swelling +GSK205, sample ×4 Wildtype, loaded 24 hours +GSK205, sample ×4 Wildtype, loaded 0 hours +GSK205, sample ×4 V620I, free-swelling, sample ×4 V620I, loaded 24 hours, sample ×4 +10 more

Supports a between-group comparison across 71 samples.

How we read this: 18 replicated groups read from 71 sample titles; they account for 71 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 31 more — browse all 71 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.